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- PDB-6v3y: Crystal structure of EED in complex with PALI1-K1219me3 peptide -

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Basic information

Entry
Database: PDB / ID: 6v3y
TitleCrystal structure of EED in complex with PALI1-K1219me3 peptide
Components
  • PALI1 peptide
  • Polycomb protein EED
KeywordsGENE REGULATION / EED / PALI1 / tri-methyl-lysine / LCOR / C10ORF12
Function / homology
Function and homology information


regulation of adaxial/abaxial pattern formation / sex chromatin / facultative heterochromatin formation / genomic imprinting / ESC/E(Z) complex / chromatin silencing complex / pronucleus / spinal cord development / Transcriptional Regulation by E2F6 / : ...regulation of adaxial/abaxial pattern formation / sex chromatin / facultative heterochromatin formation / genomic imprinting / ESC/E(Z) complex / chromatin silencing complex / pronucleus / spinal cord development / Transcriptional Regulation by E2F6 / : / oligodendrocyte differentiation / cellular response to leukemia inhibitory factor / Regulation of PTEN gene transcription / transcription corepressor binding / PRC2 methylates histones and DNA / Defective pyroptosis / enzyme activator activity / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / heterochromatin formation / Oxidative Stress Induced Senescence / negative regulation of DNA-templated transcription / chromatin binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
: / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsZhang, Q. / Davidovich, C.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE180100219 Australia
Australian Research Council (ARC)DP190103407 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1162921 Australia
Citation
Journal: Nat Commun / Year: 2021
Title: PALI1 facilitates DNA and nucleosome binding by PRC2 and triggers an allosteric activation of catalysis.
Authors: Zhang, Q. / Agius, S.C. / Flanigan, S.F. / Uckelmann, M. / Levina, V. / Owen, B.M. / Davidovich, C.
#1: Journal: Nat Commun / Year: 2021
Title: PALI1 facilitates DNA and nucleosome binding by PRC2 and triggers an allosteric activation of catalysis
Authors: Zhang, Q. / Aguis, S.C. / Flanigan, S.F. / Uckelmann, M. / Levina, V. / Owen, B.M. / Davidovich, C.
History
DepositionNov 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polycomb protein EED
B: PALI1 peptide


Theoretical massNumber of molelcules
Total (without water)42,0402
Polymers42,0402
Non-polymers00
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-6 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.775, 85.296, 91.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Polycomb protein EED / hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic ...hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1


Mass: 41374.988 Da / Num. of mol.: 1 / Fragment: UNP residues 81-439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Escherichia coli (E. coli) / References: UniProt: O75530
#2: Protein/peptide PALI1 peptide


Mass: 664.813 Da / Num. of mol.: 1 / Fragment: residues 1217-1221 / Source method: obtained synthetically / Details: UNP Q96JN0-3 / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.6 M sodium formate, 10 mM TCEP, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.63→48.79 Å / Num. obs: 57098 / % possible obs: 99.7 % / Redundancy: 8.1 % / Biso Wilson estimate: 16.94 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.2
Reflection shellResolution: 1.63→1.71 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.643 / Num. unique obs: 8025 / CC1/2: 0.866 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
PHENIX1.17.1_3660refinement
XDSdata processing
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3JZN

3jzn


Resolution: 1.63→48.79 Å / SU ML: 0.162 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.3471
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1925 2824 4.95 %
Rwork0.1651 54198 -
obs0.1665 57022 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.89 Å2
Refinement stepCycle: LAST / Resolution: 1.63→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 0 267 3155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573017
X-RAY DIFFRACTIONf_angle_d0.89024102
X-RAY DIFFRACTIONf_chiral_restr0.0609441
X-RAY DIFFRACTIONf_plane_restr0.0053528
X-RAY DIFFRACTIONf_dihedral_angle_d6.3059405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.660.27771210.24682573X-RAY DIFFRACTION93.9
1.66-1.690.26721390.2062657X-RAY DIFFRACTION100
1.69-1.720.22921440.20352700X-RAY DIFFRACTION100
1.72-1.750.22561400.18742662X-RAY DIFFRACTION100
1.75-1.790.20941360.18412676X-RAY DIFFRACTION100
1.79-1.830.22241500.17152673X-RAY DIFFRACTION100
1.83-1.880.18831340.17552682X-RAY DIFFRACTION99.86
1.88-1.930.18481410.15592716X-RAY DIFFRACTION100
1.93-1.990.1861120.15862709X-RAY DIFFRACTION100
1.99-2.050.17611460.16052692X-RAY DIFFRACTION99.96
2.05-2.120.19691480.15592696X-RAY DIFFRACTION100
2.12-2.210.20211340.15612696X-RAY DIFFRACTION100
2.21-2.310.17861540.16472701X-RAY DIFFRACTION100
2.31-2.430.18931330.17372724X-RAY DIFFRACTION100
2.43-2.580.23161530.17782711X-RAY DIFFRACTION100
2.58-2.780.19411510.18822724X-RAY DIFFRACTION100
2.78-3.060.19731280.17992753X-RAY DIFFRACTION100
3.06-3.510.19781330.15762770X-RAY DIFFRACTION100
3.51-4.420.17761550.13162777X-RAY DIFFRACTION100
4.42-48.790.16191720.16112906X-RAY DIFFRACTION99.94

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